Abstract 6602: Refining liquid biopsy: generating more information from cell free DNA
Authors: Fabio Puddu, Casper K. Lumby, Nick Harding, David J. Morley, Jamie Scotcher, Robert Crawford, Jens Füllgrabe, Walraj S. Gosal, Shirong Yu, Daniel Brudzewsky, Jane Haywood, Andrada Tomoni, Philippa Burns, Joanna D. Holbrook, Paidi Creed
Journal: Cancer Research (2023)

Abstract Liquid biopsy for profiling of cell free DNA (cfDNA) in blood holds huge promise to transform how we experience and manage cancer by early detection and identification of residual disease and subtype. However, a standard blood draw yields an average of only 10 ng of cfDNA, of which DNA derived from the tumor is a small minority. Therefore, we are faced with a dilemma when utilizing the limited sample to obtain maximum information. Genetic sequencing provides information on actionable somatic mutations but detection of a few loci in a minority of the sample is challenging. Modified cytosine profiles of cancer are differential from non-cancer at many more loci and so provide a stronger signal. Moreover, they can be used to distinguish tissue-of-origin of the tumor. However, methods such as bisulfite sequencing, EM-seq and TAPS sacrifice genetic information (namely C-&amp;gt;T mutations, which are the most common mutation in cancer) to measure modified cytosine. Genetic and modified cytosine data together have been shown to be more powerful for the detection of early cancer than either alone. Here we present a technology, which sequences at base resolution the complete genetic sequence integrated with modified cytosine from low nanogram amounts of cfDNA. It consists of (i) a single pre-sequencing workflow, which creates a copy of the original DNA and performs enzymatic base conversions which discriminate genetic and epigenetic states and (ii) post-sequencing data processing which resolves the resultant sequencing data to an information-rich 16-state code and derives genetic variants integrated with modified cytosine levels, within easy-to-use software. It is, in principle, compatible with any sequencing methodology and is shown here optimized for the Illumina fleet. In cfDNA we show accuracy of modC measurement is higher than that of bisulfite sequencing and EM-seq; and the accuracy of genetic sequencing is higher than that of Illumina alone. Accuracy of measurement is extremely important for liquid biopsy where tumor DNA is in the minority and observed in a small number of reads. We demonstrate the impact of varying base calling error rate on limit of detection for rare alleles in cfDNA samples. Further we show derivation of cfDNA fragment characteristics and that this is produced in combination with genetic and modC information. This further increases the signal available from cfDNA in only one workflow. We suggest this method will help advance the field of liquid biopsy towards its promise. Citation Format: Fabio Puddu, Casper K. Lumby, Nick Harding, David J. Morley, Jamie Scotcher, Robert Crawford, Jens Füllgrabe, Walraj S. Gosal, Shirong Yu, Daniel Brudzewsky, Jane Haywood, Andrada Tomoni, Philippa Burns, Joanna D. Holbrook, Paidi Creed. Refining liquid biopsy: generating more information from cell free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6602.